rs10805117

Variant names:

• chr4-40330821-T-A
• rs10805117

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.205 in 152,114 control chromosomes in the GnomAD database, including 3,642 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.20 (3642 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31150 AN: 151996 Hom.: 3644 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.211

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.205 AC: 31149 AN: 152114 Hom.: 3642 Cov.: 32 AF XY: 0.208 AC XY: 15452 AN XY: 74340

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.209

Alfa AF: 0.220 Hom.: 528

Bravo AF: 0.202

Asia WGS AF: 0.164 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.85

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10805117; hg19: chr4-40332838;